Scientific Program

Abstract:

The protein diversity of mammalian cells is determined by arrays of isoforms from genes. Genetic mutation is essential in species evolution and cancer development. Accurate Long-read transcriptome sequencing at single-cell level is required to decipher the spectrum of protein expressions in mammalian organisms. In this report, we developed a synthetic long-read single-cell sequencing technology based on LOOPseq technique. We applied this technology to analyze 447 transcriptomes of hepatocellular carcinoma (HCC) and benign liver from an individual. Through Uniform Manifold Approximation and Projection (UMAP) analysis, we identified a panel of mutation mRNA isoforms highly specific to HCC cells. The evolution pathways that led to the hyper-mutation clusters in single human leukocyte antigen (HLA) molecules were identified. Novel fusion transcripts were detected. The combination of gene expressions, fusion gene transcripts, and mutation gene expressions significantly improved the classification of liver cancer cells versus benign hepatocytes. In conclusion, LOOPseq single-cell technology may hold promise to provide a new level of precision analysis on the mammalian transcriptome.

Audience Take Away Notes:

• Mutation is the fundamental cause of human liver cancer
• Mutations evolve from a single nucleotide alteration of specific region in the HLA molecules and expanded to spread to other regions of the same alleles
• Hypermutation clusters are readily identified in HLA molecules that may be essential for cancer cells to evade immune surveillance

Biography:

Dr. Luo has been studying molecular mechanisms of human malignancies in the last 35 years. Currently, he is a Professor of Pathology and Director of High Throughput Genome Center at University of Pittsburgh. In the last 29 years, Dr. Luo has been largely focusing on the genetic and molecular mechanism of human cancers such as prostate cancer. He is one of the pioneers in utilizing high throughput gene expression and genome analyses to analyze field effects in prostate cancer and liver cancer. He is also the first in using methylation array and whole genome methylation sequencing to analyze prostate cancer. He and his colleague helped to develop an ultra-low error synthetic long-read sequencing technology called LOOPSeq that can be utilized to quantify mRNA isoforms and mutation isoform distributions in single cell level. His group has discovered 21 novel fusion genes in prostate, liver and colon cancers. Subsequently, his group discovered that many of these fusion genes are recurrent in many other types of human cancers. His group also developed a genome intervention strategy targeting at the chromosomal breakpoint of fusion gene to treat cancers. Overall, these findings advance our understanding of how cancer develops and behaves, and lay down the foundation for better future diagnosis and treatment for human malignancies